Quin will remain in Wellington and isn't seeking another corporate role, although she won't rule it out, but would prefer a couple of directorships along with the board position she took in May with Westpac NZ.
Informed sources, who spoke on condition they weren't identified, say her own board deemed her a capable manager rather than the visionary leader it wanted to drive Callaghan's new strategy.
The resignation was announced by deputy chairman Robin Hapi rather than chairwoman Sue Suckling, who was overseas at the time. Hapi's comments about reaching a confidential agreement with Quin and that she left with the company's best wishes rather than regret fanned speculation about the departure.
Suckling later said the board had been talking with Quin "for some time about the future of the organisation" which culminated in her resigning. "Mary did a good job in setting up the organisation and is now going to do other things." Quin declined to comment.
Both Suckling and Science and Innovation Minister Steven Joyce, who oversees Callaghan, are said to have interventionist management styles. Joyce previously described Quin as "nuggety and feisty" and she admits to being "feisty".
While avoiding direct comment on tensions with the board, Quin says she had autonomy to bring the organisation to the level it's now at.
"This gives the board the opportunity to bring in leadership that will take it to a whole other level and that will be exciting to watch."
Judging Quin's performance along with that of Callaghan over the past three years isn't easy. It gave $138 million in grants last year and its revenue in the 2016/17 financial year is expected to be almost $300m.
Statistics New Zealand figures show there are about 50,000 manufacturing and digital service companies, of which only about 5000 employ more than five people.
"New Zealand's challenge is that it is a country of SMEs, but not small to medium enterprises - small to micro enterprises," Quin says. "The whole purpose of the creation of Callaghan Innovation is how to help more of those companies grow bigger, faster and to be ambitious."
One change in the strategy will be more focus on sectors that have potential to become global market leaders and where exciting New Zealand companies and entrepreneurs are already active - medical devices, unmanned aerial vehicles, value-add food and beverage products, agri-tech, and parts of the energy sector.
There will also be more investment in Callaghan's science and technical capability, and its relationships with other research and development providers. Early on, Quin shifted the focus of the research team she inherited from the former Industrial Research Ltd away from blue-sky research and competing for contestable science funding. "Our focus is on small R and big D. That's where businesses need our help."
How well that science capability is working within an agency seen from the outside as largely charged with research and development funding remains an open question in the science community. Quin says it's still at the start of that journey.
"It takes time to take the talent we have in the organisation and make sure those individuals are excited about and involved in that kind of work and then by engaging with companies to see what are the areas of research or technical expertise they need that we don't have.
"That's not just a multi-year but a multi-decade project."
Suckling agrees with outside criticism that the organisation's R&D side hasn't yet been well-integrated. "That's another area for future work".
Callaghan is still progressing the business case required for Treasury and Government approval to develop IRL's Gracefield campus into an Innovation Precinct. Callaghan had $54.9m in capital at the end of June, much of which is likely to be drawn down for upgrading and expanding the run-down facilities. That's likely to be augmented by some form of public/private partnership, Quin said. Around two dozen companies are already co-located with Callaghan's R&D staff on the Lower Hutt campus, which also houses Victoria University's Ferrier and Robinson Institutes.
After talking to Kiwi businesses and staff internally, Callaghan's strategic refresh focuses on becoming more customer responsive and co-creation in R&D. Quin says there's been progress on the overall mission of business growth and R&D spend although it's a job that's "never done".
BusinessDesk receives assistance from Callaghan Innovation to help cover the commercialisation of innovation.